I have a position-specific weight matrix for a class of protein. Each position has an associated probability for all 20 amino acids being found at that position. How can I convert this weight matrix to a psiblast-compatible PSSM file (to enable use as a query against a sequence database to find sequences that match my profile).

I also welcome suggestions on other methods to search a position-specific weight matrix against a sequence database. I want to be able to make use of the probabilities in the matrix for scoring against the database, not just consider the highest-probability residue at each position. And I'd like to allow for gapped alignment of my profile against target sequences.